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Homology modeling by the ICM method.
Cardozo T, Totrov M, Abagyan R. Cardozo T, et al. Among authors: totrov m. Proteins. 1995 Nov;23(3):403-14. doi: 10.1002/prot.340230314. Proteins. 1995. PMID: 8710833
Structural genomics for drug design against the pathogen Coxiella burnetii.
Franklin MC, Cheung J, Rudolph MJ, Burshteyn F, Cassidy M, Gary E, Hillerich B, Yao ZK, Carlier PR, Totrov M, Love JD. Franklin MC, et al. Among authors: totrov m. Proteins. 2015 Dec;83(12):2124-36. doi: 10.1002/prot.24841. Epub 2015 Oct 6. Proteins. 2015. PMID: 26033498
Contact area difference (CAD): a robust measure to evaluate accuracy of protein models.
Abagyan RA, Totrov MM. Abagyan RA, et al. Among authors: totrov mm. J Mol Biol. 1997 May 9;268(3):678-85. doi: 10.1006/jmbi.1997.0994. J Mol Biol. 1997. PMID: 9171291
Flexible protein-ligand docking by global energy optimization in internal coordinates.
Totrov M, Abagyan R. Totrov M, et al. Proteins. 1997;Suppl 1:215-20. doi: 10.1002/(sici)1097-0134(1997)1+<215::aid-prot29>3.3.co;2-i. Proteins. 1997. PMID: 9485515
., Totrov, M.M. J. Mol. Biol. 235: 983-1002, 1994]. The procedure uses two types of efficient random moves, a pseudobrownian positional move [Abagyan, R.A., Totrov, M.M., Kuznetsov, D.A. ...Chem. 15:488-506, 1994] and a Biased-Probability …
., Totrov, M.M. J. Mol. Biol. 235: 983-1002, 1994]. The procedure uses two types of efficient random moves, a pseudobro …
Homology modeling with internal coordinate mechanics: deformation zone mapping and improvements of models via conformational search.
Abagyan R, Batalov S, Cardozo T, Totrov M, Webber J, Zhou Y. Abagyan R, et al. Among authors: totrov m. Proteins. 1997;Suppl 1:29-37. doi: 10.1002/(sici)1097-0134(1997)1+<29::aid-prot5>3.3.co;2-4. Proteins. 1997. PMID: 9485492
., Totrov, M.J. Mol. Biol. 268:678-685, 1997]. The CAD measure is proposed for ranking models built by homology instead of global root-mean-square deviation, which is frequently dominated by insignificant yet large contributions from incorrectly predicted fragments …
., Totrov, M.J. Mol. Biol. 268:678-685, 1997]. The CAD measure is proposed for ranking models built by homology instead of glo …
The contour-buildup algorithm to calculate the analytical molecular surface.
Totrov M, Abagyan R. Totrov M, et al. J Struct Biol. 1996 Jan-Feb;116(1):138-43. doi: 10.1006/jsbi.1996.0022. J Struct Biol. 1996. PMID: 8742735
Prediction of the binding energy for small molecules, peptides and proteins.
Schapira M, Totrov M, Abagyan R. Schapira M, et al. Among authors: totrov m. J Mol Recognit. 1999 May-Jun;12(3):177-90. doi: 10.1002/(SICI)1099-1352(199905/06)12:3<177::AID-JMR451>3.0.CO;2-Z. J Mol Recognit. 1999. PMID: 10398408 Review.
Improving CAPRI predictions: optimized desolvation for rigid-body docking.
Fernández-Recio J, Abagyan R, Totrov M. Fernández-Recio J, et al. Among authors: totrov m. Proteins. 2005 Aug 1;60(2):308-13. doi: 10.1002/prot.20575. Proteins. 2005. PMID: 15981266
PIER: protein interface recognition for structural proteomics.
Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R. Kufareva I, et al. Among authors: totrov m. Proteins. 2007 May 1;67(2):400-17. doi: 10.1002/prot.21233. Proteins. 2007. PMID: 17299750
Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.
Arnautova YA, Abagyan RA, Totrov M. Arnautova YA, et al. Among authors: totrov m. Proteins. 2011 Feb;79(2):477-98. doi: 10.1002/prot.22896. Proteins. 2011. PMID: 21069716 Free PMC article.
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